I noticed at some point this message started popping up (I think after 3.0).
A script named ‘MyClass.cs’ already exists at {some other directory/namespace/MyClass.cs}. Please rename one of the scripts to a unique name.
Why? I understand what the error means ultimately, I am just not sure I understand the rationale behind the additional restriction. It’s not a C# “CSxxxx” message so I assume this is a restriction that Unity has placed on top of Mono for some reason. Of course, C# allows this as long as the classes are in different namespaces.
Edit for clarification: It is true that classes extending MonoBehaviours cannot have the same name because of the fact that they are required to be in the default namespace and are thus not allowed to. This is noted in the documentation. That is presumably caused by some problem they have not worked around in the engine I suppose. The classes that I am speaking of are just plain classes and do not have these requirements.
Edit 10/8/11 - After talking with the Unity engineers it seems that this was a bit of overstepping on the code that checks script names that are MonoBehaviours. MonoBehaviours cannot be in a namespace and have to be in a file that’s the same name as the class so this makes sense for them but not for other packaged (not Monobehaviour) classes. So I guess at this time it’s a feature.